Construction of a ball-and-spike protein supramolecule.
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Amino Acid Sequence↗
Biomedical subjects
Ichiro Yamashita
Publications and source records attributed to Ichiro Yamashita.
Monitoring of vasculogenesis-inhibiting activities in sewage effluents by using medaka embryos.
Environmental samples are known to be contaminated with complex chemicals such as estrogens, polycyclic aromatic hydrocarbons, and retinoids. These contaminants have potentially an adverse impact on survival of aquatic animals, because we found previously that medaka (Oryzias latipes) embryos are defective in the development of blood vessels and bones in the presence of these chemicals. Thus, it is important to test whether sewage effluents contain inhibitory activities against the embryonic development. To examine for such activity, medaka embryos were exposed for 48 h to extracts or freeze-evaporated concentrates of effluent samples collected from different municipal sewage treatment plants. We used the transgenic embryos that are hypersensitive to estrogens due to a high-level expression of estrogen receptor for detecting the total (sum of estrogenic and non-estrogenic) vessel-inhibiting activity. The embryos were specifically defective in blood-vessel formation in most effluent samples, showing the activities ranging from 3 to 30 ng of 17beta-estradiol equiv per liter. Detection limit of 17beta-estradiol was 10 ng per liter. For detection of the non-estrogenic vessel-inhibiting activity, we treated the transgenic embryos in the presence of an antiestrogen, tamoxifen, or used the wild-type embryos. The non-estrogenic activities were found in some (7 out of 18) effluents, ranging from half to all of the total activities. Our findings for the first time demonstrate the utility of the vascular assay for monitoring sewage effluents.
Animals↗
Selective nanoscale positioning of ferritin and nanoparticles by means of target-specific peptides.
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Adsorption↗
Rounding up: Engineering 12-membered rings from the cyclic 11-mer TRAP.
The protein TRAP (trp RNA binding attenuation protein) forms a highly thermostable ring-shaped 11-mer. By linking in tandem two, three, or four DNA sequences encoding TRAP monomers, we have engineered new rings that consist of 12 TRAP subunits and bind 12 ligand molecules. The hydrogen bonding pattern and buried surface area within and between subunits are essentially identical between the 11-mer and 12-mer crystal structures. Why do the artificial proteins choose to make single 12-mer rings? The 12-mer rings are highly sterically strained by their peptide linkers and far from thermostable. That proteins choose to adopt a strained conformation of few subunits rather than an unstrained one with 11 subunits demonstrates the importance of entropic factors in controlling protein-protein interactions in general.
Bacterial Proteins↗
Mechanism underlying specificity of proteins targeting inorganic materials.
Adhesion force analysis using atomic force microscopy clearly revealed for the first time the mechanism underlying the specific binding between a titanium surface and ferritin possessing the sequence of Ti-binding peptide in its N-terminal domain. Our results proved that the specific binding is due to double electrostatic bonds between charged residue and surface groups of the substrate. Furthermore, it is also demonstrated that the accretion of surfactant reduces nonspecific interactions, dramatically enhancing the selectivity and specificity of Ti-binding peptide.
Amino Acid Sequence↗
DNA secondary structure forming at minisatellite repeat unit sequences.
The lengths of simple repeat sequences are generally unstable or polymorphic; that is, they are highly variable with respect to the numbers of tandem repeats. To determine the structural features that cause such variability, we examined a minisatellite DNA isolated from the yellow fin sea bream Acanthopagrus latus. Electrophoresis, CD spectra, and calorimetric analyses of oligodeoxyribonucleotides comprised of the minisatellite repeat unit suggest a stable secondary structure is formed within the repeat unit.
Animals↗
Fabrication of ZnSe nanoparticles in the apoferritin cavity by designing a slow chemical reaction system.
Zinc selenide nanoparticles (ZnSe NPs) were synthesized in the cavity of the cage-shaped protein apoferritin by designing a slow chemical reaction system, which employs tetraaminezinc ion and selenourea. The chemical synthesis of ZnSe NPs was realized in a spatially selective manner from an aqueous solution, and ZnSe cores were formed in almost all apoferritin cavities with little bulk precipitation. Three factors are found to be important for ZnSe NP synthesis in the apoferritin cavity: (1) the threefold channel, which selectively introduces zinc ion into the apoferritin cavity, (2) the apoferritin internal potential, which favors zinc ion accumulation in the cavity, and (3) the nucleation site, which nucleates ZnSe inside the cavity. The characterization of the synthesized ZnSe NPs by X-ray powder diffraction and energy-dispersive spectrometry revealed that the synthesized NPs are a collection of cubic ZnSe polycrystals. It was shown that the 500 degrees C heat treatment for 1 h under nitrogen gas transformed the polycrystalline ZnSe core into a single crystal, and single-crystal ZnSe NPs free of protein were obtained.
Journal Article↗
Endowing a ferritin-like cage protein with high affinity and selectivity for certain inorganic materials.
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Ferritins↗
Nuclear localization and interaction of RolB with plant 14-3-3 proteins correlates with induction of adventitious roots by the oncogene rolB.
The rooting-locus gene B (rolB) on the T-DNA of the root-inducing (Ri) plasmid in Agrobacterium rhizogenes is responsible for the induction of transformed adventitious roots, although the root induction mechanism is unknown. We report here that the RolB protein of pRi1724 (1724RolB) is associated with Nicotianatabacum14-3-3-like protein omegaII (Nt14-3-3 omegaII) in tobacco bright yellow (BY)-2 cells. Nt14-3-3 omegaII directly interacts with 1724RolB protein. Green fluorescent protein (GFP)-fused 1724RolB is localized to the nucleus. GFP-fused mutant 1724RolB proteins having a deletion or amino acid substitution are unable to interact with Nt14-3-3 omegaII and also show impaired nuclear localization. Moreover, these 1724RolB mutants show decreased capacity for adventitious root induction. These results suggest that adventitious root induction by 1724RolB protein correlates with its interaction with Nt14-3-3 omegaII and the nuclear localization of 1724RolB protein.
14-3-3 Proteins↗
Retionic acid and its receptors are required for expression of aryl hydrocarbon receptor mRNA and embryonic development of blood vessel and bone in the medaka fish, Oryzias latipes.
Retinoic acid (RA), the active derivative of vitamin A, is essential for normal embryonic development of vertebrates because both the lack and excess of RA result in developmental malformations. We previously reported that aryl hydrocarbon receptor (AHR) is also required for vascular and bone formation by regulating cytochrome P450 expression. However, little is known about the roles of retinoic acid receptors (RAR) and retinoid X receptors (RXR) in the embryonic development of blood vessels and molecular cross-talk between RAR/RXR and AHR. We report for the first time that RA and RAR/RXR are required for expression of AHR mRNA and the embryonic development of blood vessel and bone. The embryonic organogenesis of medaka fish was specifically inhibited by an inhibitor of RA synthesis (diethylaminobenzaldehyde), antagonists of RAR (Ro41-5253) and RXR (Ro71-4595), agonist (beta-naphthoflavone) and antagonist (alpha-naphthoflavone) of AHR, and excess RA. These reagents are useful for future studies to elucidate molecular mechanisms for vascular and bone formation in the medaka embryogenesis. Our results also show that medaka embryos may be useful for screening inhibitors of vascular formation for anti-cancer drugs.
Animals↗
Fabrication of nickel and chromium nanoparticles using the protein cage of apoferritin.
The iron storage protein, apoferritin, has a cavity in which iron is oxidized and stored as a hydrated oxide core. The size of the core is about 7 nm in diameter and is regulated by the cavity size. The cavity can be utilized as a nanoreactor to grow inorganic crystals. We incubated apoferritin in nickel or chromium salt solutions to fabricate hydroxide nanoparticles in the cavity. By using a solution containing dissolved carbon dioxide and by precisely controlling the pH, we succeeded in fabricating nickel and chromium cores. During the hydroxylation process of nickel ions a large portion of the apoferritin precipitated through bulk precipitation of nickel hydroxide. Bulk precipitation was suppressed by adding ammonium ions. However, even in the presence of ammonium ions the core did not form using a degassed solution. We concluded that carbonate ions were indispensable for core formation and that the ammonium ions prevented precipitation in the bulk solution. The optimized condition for nickel core formation was 0.3 mg/mL horse spleen apoferritin and 5 mM ammonium nickel sulfate in water containing dissolved carbon dioxide. The pH was maintained at 8.65 using two buffer solutions: 150 mM HEPES (pH 7.5) and 195 mM CAPSO (pH 9.5) with 20 mM ammonium at 23 degrees C. The pH had not changed after 48 h. After 24 h of incubation, all apoferritins remained in the supernatant and all of them had cores. Recombinant L-ferritin showed less precipitation even above a pH of 8.65. A chromium core was formed under the following conditions: 0.1 mg/mL apoferritin, 1 mM ammonium chromium sulfate, 100 mM HEPES (pH 7.5) with a solution containing dissolved carbon dioxide. About 80% of the supernatant apoferritin (0.07 mg/mL) formed a core. In nickel and chromium core formation, carbonate ions would play an important role in accelerating the hydroxylation in the apoferritin cavity compared to the bulk solution outside.
Alkanesulfonic Acids↗
No effects of estrogen receptor overexpression on gonadal sex differentiation and reversal in medaka fish.
In order to elucidate a possible role of estrogen receptor in the gonadal sex differentiation and the sex reversal with sex steroids, we examined for the formation of testis or ovary in transgenic medaka fish overexpressing the medaka estrogen receptor under the constitutive medaka beta-actin promoter. The transgenic fish underwent the genetically determined gonadal differentiation and showed the same sex-reversal rates as those of wild-type non-transgenic fish after treatments with estrogen and androgen. These results present invaluable data to reconsider the role of estrogen receptor in the gonadal sex determination.
Androgens↗
Phosphatidylinositol 3-phosphate 5-kinase is required for the cellular response to nutritional starvation and mating pheromone signals in Schizosaccharomyces pombe.
BACKGROUND: Phosphatidylinositol (3,5) bisphosphate, which is converted from phosphatidylinositol 3-phosphate by phosphatidylinositol 3-phosphate 5-kinase, is implicated in vacuolar functions and the sorting of cell surface proteins within endosomes in the endocytic pathway of budding yeast. A homologous protein, SpFab1p, has been found in the fission yeast Schizosaccharomyces pombe, but its role is not known. RESULTS: Here we report that SpFab1p is encoded by ste12+ known as a fertility gene in S. pombe. The ste12 mutant grew normally under stress-free conditions, but was highly vacuolated and swelled at high temperatures and under starvation conditions. In nitrogen-free medium, ste12 cells were arrested in G1 phase, but partially defective in the expression of genes responsible for mating and meiosis. The ste12 mutant was defective both in the production of, and in the response to, mating pheromones. The amount of the pheromone receptor protein Map3p, was substantially decreased in ste12 cells. Map3p was transported to the cell surface, then internalized and eventually transported to the vacuolar lumen, even in the ste12 mutant. CONCLUSION: The results indicate that phosphatidylinositol(3,5)bisphosphate is essential for cellular responses to various stresses and for the mating pheromone signalling under starvation conditions.
Amino Acid Sequence↗
Tobacco plants were transformed by Agrobacterium rhizogenes infection during their evolution.
We discovered that the origin of cT-DNA in the genome of wild-type Nicotiana glauca is the T-DNA of the mikimopine-type Ri plasmid (pRi) harbored in Agrobacterium rhizogenes. The cT-DNA was inserted into the genomic DNA of N. glauca from the position corresponding to the right border of mikimopine-type pRi. The cT-DNA contained two mikimopine synthase gene (mis) homologs, NgmisL and NgmisR, both of which were transcribed at low level in all N. glauca organs. NgMisR protein expressed in Escherichia coli has preserved Mis activity, which converts l-histidine and alpha-ketoglutaric acid to mikimopine. The mis homolog was also found in the genome of three other Nicotiana species: N. tomentosa, N. tomentosiformis, and N. tabacum; however, the site of insertion differed from that in N. glauca, suggesting that A. rhizogenes harboring mikimopine-type pRi independently infected the ancestors of some Nicotiana plants. This is the first clear evidence of a host-parasite relationship during the early evolution of Nicotiana plants. We propose that a new phylogenetic approach using opine type cT-DNA is applicable for presuming divergence in the genus Nicotiana.
Amino Acid Sequence↗
Estrogen inhibits development of yolk veins and causes blood clotting in transgenic medaka fish overexpressing estrogen receptor.
We established three transgenic medaka fish lines overexpressing the medaka estrogen receptor under the constitutive medaka beta-actin promoter. The transgenic embryos became hypersensitive to estrogens (17 beta-estradiol and 17alpha-ethinylestradiol), and failed to develop yolk veins while blood clots formed in the blood island within 3 days after exposure to the estrogens. The embryos developed normally if exposed to estrogen after an early neurula stage, suggesting that the sensitive stage is before neurulation. The developmental defects were recovered by incubation with an anti-estrogen, tamoxifen. These results indicate that activation of estrogen receptor caused the estrogen-induced developmental defects. Our results show that the transgenic embryos can be used to assay the blood clotting activity of estrogenic compounds in vivo.
Animals↗
Aryl hydrocarbon receptor is required for prevention of blood clotting and for the development of vasculature and bone in the embryos of medaka fish, Oryzias latipes.
The aryl hydrocarbon receptor (AHR) is a member of ligand-activated transcription factors and conserved among vertebrates. To investigate the role of AHR in fish development, medaka embryos were treated with agonist (2,3,7,8-tetrachlorodibenzo-p-dioxin), antagonists (alpha-naphthoflavone and resveratrol), and inhibitor (piperonyl butoxide) of cytochromes (Cyts) P450 encoded by a battery of target genes. These embryos were found to have similar abnormal phenotypes. Among the most consistent phenotypes were blood clotting and malformation of bone that were associated with vascular damages. These results thus indicate that control of AHR is important for proper development of fish embryos. AHR may control levels of Cyts P450 that are responsible for synthesis and metabolism of a toxic compound that caused the abnormal phenotypes. Complementary DNA fragments encoding AHR homologs were cloned from medaka embryos. AHR-specific mRNA was ubiquitously expressed in embryos and adult tissues.
Acetylcysteine↗